tbuckley/cabot-search huggingface dataset:
Mapping brain gene coexpression in daytime transcriptomes unveils diurnal molecular networks and deciphers perturbation gene signatures
Authors: Nan Wang, Peter Langfelder, Matthew Stricos, Lalini Ramanathan, Jeffrey B. Richman, Raymond Vaca, Mary Plascencia, Xiaofeng Gu, Shasha Zhang, T. Katherine Tamai, Liguo Zhang, Fuying Gao, Koliane Ouk, Xiang Lu, Leonid V. Ivanov, Thomas F. Vogt, Qing Richard Lu, A. Jennifer Morton, Christopher S. Colwell, Jeffrey S. Aaronson, Jim Rosinski, Steve Horvath, X. William Yang
Journal: Neuron (2022)

Brain tissue transcriptomes may be organized into gene coexpression networks, but their underlying biological drivers remain incompletely understood. Here, we undertook a large-scale transcriptomic study using 508 wild-type mouse striatal tissue samples dissected exclusively in the afternoons to define 38 highly reproducible gene coexpression modules. We found that 13 and 11 modules are enriched in cell-type and molecular complex markers, respectively. Importantly, 18 modules are highly enriched in daily rhythmically expressed genes that peak or trough with distinct temporal kinetics, revealing the underlying biology of striatal diurnal gene networks. Moreover, the diurnal coexpression networks are a dominant feature of daytime transcriptomes in the mouse cortex. We next employed the striatal coexpression modules to decipher the striatal transcriptomic signatures from Huntington's disease models and heterozygous null mice for 52 genes, uncovering novel functions for Prkcq and Kdm4b in oligodendrocyte differentiation and bipolar disorder-associated Trank1 in regulating anxiety-like behaviors and nocturnal locomotion.
Neoadjuvant immunotherapy, chemotherapy, and combination therapy in muscle-invasive bladder cancer: A multi-center real-world retrospective study
Authors: Jiao Hu, Jinbo Chen, Zhenyu Ou, Haige Chen, Zheng Liu, Minfeng Chen, Ruiyun Zhang, Anze Yu, Rui Cao, Enchong Zhang, Xi Guo, Bo Peng, Dingshan Deng, Chunliang Cheng, Jinhui Liu, Huihuang Li, Yihua Zou, Ruoping Deng, Gang Qin, Wenze Li, Lue Wang, Tao Chen, Xiaming Pei, Guanghui Gong, Jiansheng Tang, Belaydi Othmane, Zhiyong Cai, Chunyu Zhang, Zhi Liu, Xiongbing Zu
Journal: Cell Reports Medicine (2022)

To parallelly compare the efficacy of neoadjuvant immunotherapy (tislelizumab), neoadjuvant chemotherapy (gemcitabine and cisplatin), and neoadjuvant combination therapy (tislelizumab + GC) in patients with muscle-invasive bladder cancer (MIBC) and explore the efficacy predictors, we perform a multi-center, real-world cohort study that enrolls 253 patients treated with neoadjuvant treatments (combination therapy: 98, chemotherapy: 107, and immunotherapy: 48) from 15 tertiary hospitals. We demonstrate that neoadjuvant combination therapy achieves the highest complete response rate and pathological downstaging rate compared with neoadjuvant immunotherapy or chemotherapy. We develop and validate an efficacy prediction model consisting of pretreatment clinical characteristics, which can pinpoint candidates to receive neoadjuvant combination therapy. We also preliminarily reveal that patients who achieve pathological complete response after neoadjuvant treatments plus maximal transurethral resection of the bladder tumor may be safe to receive bladder preservation therapy. Overall, this study highlights the benefit of neoadjuvant combination therapy based on tislelizumab for MIBC.
Efficacy and Safety of Ketamine vs Electroconvulsive Therapy Among Patients With Major Depressive Episode
Authors: Taeho Greg Rhee, Sung Ryul Shim, Brent P. Forester, Andrew A. Nierenberg, Roger S. McIntyre, George I. Papakostas, John H. Krystal, Gerard Sanacora, Samuel T. Wilkinson
Journal: JAMA Psychiatry (2022)

Whether ketamine is as effective as electroconvulsive therapy (ECT) among patients with major depressive episode remains unknown.
Intraoperative Urinary Catheter Use and Risk of Postoperative Urinary Retention
Authors: Jinfeng Wu, Jian Chen, Qiang Hu
Journal: JAMA Surgery (2022)

To the Editor We are glad to study the article by Fafaj et al,1 which supports the previous finding that “intraoperative urinary catheters did not reduce the risk of PUR [postoperative urinary retention] after laparoscopic inguinal hernia repair.”1 Here are some queries we have for the authors.
Defining Essential Surgery in the US During the COVID-19 Pandemic Response
Authors: Aviva S. Mattingly, Hyrum S. Eddington, Liam Rose, Arden M. Morris, Amber W. Trickey, Mark R. Cullen, Sherry M. Wren
Journal: JAMA Surgery (2022)

This cohort study compares the volume of performed surgical procedures classified as essential, urgent, and nonurgent before and after elective surgeries were restricted during the COVID-19 pandemic in the US.
Association Between Life Expectancy at Age 60 Years Before the COVID-19 Pandemic and Excess Mortality During the Pandemic in Aging Countries
Authors: Mitsuyoshi Urashima, Emiri Tanaka, Hiroto Ishihara, Taisuke Akutsu
Journal: JAMA Network Open (2022)

This cross-sectional study investigates the association between life expectancy before COVID-19 and excess mortality during the pandemic in aging countries.
Advances in the treatment of intrahepatic cholangiocarcinoma: An overview of the current and future therapeutic landscape for clinicians
Authors: Dimitrios Moris, Manisha Palta, Charles Kim, Peter J. Allen, Michael A. Morse, Michael E. Lidsky
Journal: CA A Cancer Journal for Clinicians (2022)

Abstract Intrahepatic cholangiocarcinoma (ICC) is the second most common primary liver tumor and remains a fatal malignancy in the majority of patients. Approximately 20%–30% of patients are eligible for resection, which is considered the only potentially curative treatment; and, after resection, a median survival of 53 months has been reported when sequenced with adjuvant capecitabine. For the 70%–80% of patients who present with locally unresectable or distant metastatic disease, systemic therapy may delay progression, but survival remains limited to approximately 1 year. For the past decade, doublet chemotherapy with gemcitabine and cisplatin has been considered the most effective first‐line regimen, but results from the recent use of triplet regimens and even immunotherapy may shift the paradigm. More effective treatment strategies, including those that combine systemic therapy with locoregional therapies like radioembolization or hepatic artery infusion, have also been developed. Molecular therapies, including those that target fibroblast growth factor receptor and isocitrate dehydrogenase, have recently received US Food and Drug Administration approval for a defined role as second‐line treatment for up to 40% of patients harboring these actionable genomic alterations, and whether they should be considered in the first‐line setting is under investigation. Furthermore, as the oncology field seeks to expand indications for immunotherapy, recent data demonstrated that combining durvalumab with standard cytotoxic therapy improved survival in patients with ICC. This review focuses on the current and future strategies for ICC treatment, including a summary of the primary literature for each treatment modality and an algorithm that can be used to drive a personalized and multidisciplinary approach for patients with this challenging malignancy.
Catheter-Directed Treatment of Submassive Pulmonary Embolism—A Cautious Step Closer?
Authors: Elaine M. Hylek
Journal: JAMA Cardiology (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Cardiology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Cardiology journal
Geographic Distribution and Workforce Diversity of Dermatology Physician Assistants
Authors: Peter A. Young, Cynthia F. Griffith, Rebecca Vasquez
Journal: JAMA Dermatology (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Dermatology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Dermatology journal
All Surgeons Should Be Palliative Care Surgeons
Authors: Mark R. Katlic
Journal: JAMA Surgery (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Surgery HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Surgery journal
Patient Experience Following Surgery in the Geriatric Population—Increased Relevance and Importance of Longer-Term Surgical Outcomes
Authors: Jennifer A. Perone, Daniel A. Anaya
Journal: JAMA Surgery (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Surgery HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Surgery journal
Cost-effectiveness of Response-Adapted De-escalation of Immunotherapy in Advanced Melanoma
Authors: Zachary Cartun, Wolfgang G. Kunz, Lucie Heinzerling, Dirk Tomsitz, Anne Guertler, C. Benedikt Westphalen, Jens Ricke, William Weir, Marcus Unterrainer, Dirk Mehrens
Journal: JAMA Dermatology (2022)

Combination immunotherapy with nivolumab and ipilimumab has markedly improved outcomes for patients with advanced melanoma. However, these therapies pose a considerable financial burden to both patients and the health care system. The ADAPT-IT trial demonstrated comparable progression-free and overall survival for patients with response-adapted ipilimumab discontinuation compared with standard of care (SOC).To determine the cost-effectiveness of ipilimumab discontinuation for patients with interim imaging-confirmed tumor response in the treatment of advanced melanoma.This cost-effectiveness analysis was performed using data from the ADAPT-IT (follow-up of 33 months) and CheckMate 067 (follow-up of 6.5 years) trials, as well as published literature over the ADAPT-IT trial duration of 33 months. The analysis was performed in a US setting from a US-payer perspective, and the willingness-to-pay (WTP) threshold was set at $100 000/quality-adjusted life-year (QALY). A total of 355 patients with previously untreated melanoma (unresectable stage III or IV metastatic melanoma) were included.Response-adapted ipilimumab discontinuation compared with SOC therapy.The primary outcomes of the CheckMate trial were overall survival and progression-free survival, while that of ADAPT-IT was objective response. This informed a decision model to estimate lifetime costs and QALYs associated with both strategies. Incremental cost, effectiveness, and cost-effectiveness ratio were assessed. Sensitivity and scenario analyses were performed to account for variability in trials and input parameters.Of the 355 patients included in the analysis, 41 patients were from the ADAPT-IT trial (median age, 65 years; 28 [68%] male) and 314 patients from the CheckMate 067 trial (median age, 61 years; 206 [66%] male). Response-adapted treatment was the cost-effective option in 94.0% of scenarios based on Monte Carlo simulations, with a dominant incremental cost-effectiveness ratio and an incremental net monetary benefit of $28 849 compared with SOC therapy. Cost savings were estimated at $19 891 per patient compared with SOC. In scenario analyses, current SOC was only considered as a cost-effective option under best survival assumptions and if the willingness-to-pay threshold exceeded $630 000/QALY.This economic evaluation demonstrated that response-adapted treatment de-escalation in patients with advanced melanoma may lead to considerable savings in health care costs and could represent the most cost-effective strategy across various resource settings. Future trials should aim to provide further evidence on noninferiority.
Author Correction: Pathological structural conversion of α-synuclein at the mitochondria induces neuronal toxicity
Authors: Minee L. Choi, Alexandre Chappard, Bhanu P. Singh, Catherine Maclachlan, Margarida Rodrigues, Evgeniya I. Fedotova, Alexey V. Berezhnov, Suman De, Christopher J. Peddie, Dilan Athauda, Gurvir S. Virdi, Weijia Zhang, James R. Evans, Anna I. Wernick, Zeinab Shadman Zanjani, Plamena R. Angelova, Noemi Esteras, Andrey Y. Vinokurov, Katie Morris, Kiani Jeacock, Laura Tosatto, Daniel Little, Paul Gissen, David J. Clarke, Tilo Kunath, Lucy Collinson, David Klenerman, Andrey Y. Abramov, Mathew H. Horrocks, Sonia Gandhi
Journal: Nature Neuroscience (2022)
Women Surgeon-Scientists—Applying an Intersectional Lens to the Current Status of National Institutes of Health Funding
Authors: Cherisse Berry
Journal: JAMA Surgery (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Surgery HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Surgery journal
Estimated Clinical Trial Capacity of Sites Participating in the COVID-19 Convalescent Plasma Expanded Access Program
Authors: M. Sage Gustafson, Aman Patel, Chuan Hong, Miles Meline, Daniella Peña, Charis Tang, Holly Fernandez Lynch
Journal: JAMA Network Open (2022)

This cross-sectional study estimates the trial capacity of sites participating in the COVID-19 convalescent plasma expanded access program.
Predicting DRESS Syndrome Recurrence—The ReDRESS Score
Authors: Ajay N. Sharma, Kenneth Murphy, Samantha Shwe, Melanie Miller, Natasha A. Mesinkovska, Nathan W. Rojek, Scott Worswick
Journal: JAMA Dermatology (2022)

This cross-sectional study of DRESS syndrome cases creates a model capable of predicting recurrence to identify patients most at risk.
Intraoperative Urinary Catheter Use and Risk of Postoperative Urinary Retention —Reply
Authors: Aldo Fafaj, Emanuele Lo Menzo, Michael J. Rosen
Journal: JAMA Surgery (2022)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Surgery HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Surgery journal
Adherence to the TQIP Palliative Care Guidelines Among Patients With Serious Illness at a Level I Trauma Center in the US
Authors: Jennifer Geiger Pierce, Rafael Ricon, Samveda Rukmangadhan, Matthew Kim, Ganesh Rajasekar, Miriam Nuño, Eleanor Curtis, Misty Humphries
Journal: JAMA Surgery (2022)

The American College of Surgeons Trauma Quality Improvement Program (TQIP) guidelines encourage trauma service clinicians to deliver palliative care in parallel with life-sustaining treatment and recommend goals of care (GOC) discussions within 72 hours of admission for patients with serious illness.To measure adherence to TQIP guidelines-recommended GOC discussions for trauma patients with serious illness, treated at a level I trauma center in the US.This retrospective cohort study included 674 adults admitted to a trauma service center for 3 or more days between December 2019 and June 2020. The medical records of 486 patients who met the criteria for serious illness using a consensus definition adapted to the National Trauma Data Bank were reviewed for the presence of a GOC discussion. Patients were divided into 2 cohorts based on admission before or after the guidelines were incorporated into the institutional practice guidelines on March 1, 2020.The primary outcomes were GOC completion within 72 hours of admission and during the overall hospitalization. Patient and clinical factors associated with GOC completion were assessed. Other palliative care processes measured included palliative care consultation, prior advance care planning document, and do-not-resuscitate code status. Additional end-of-life processes (ie, comfort care and inpatient hospice) were measured in a subset with inpatient mortality.Of 674 patients meeting the review criteria, 486 (72.1%) met at least 1 definition of serious illness (mean [SD] age, 60.9 [21.3] years; mean [SD] Injury Severity Score, 16.9 [12.3]). Of these patients, 328 (67.5%) were male and 266 (54.7%) were White. Among the seriously ill patients, 92 (18.9%) had evidence of GOC completion within 72 hours of admission and 124 (25.5%) during the overall hospitalization. No differences were observed between patients admitted before and after institutional guideline publication in GOC completion within 72 hours (19.0% [47 of 248 patients] vs 18.9% [45 of 238]; P = .99) or during the overall hospitalization (26.2% [65 of 248 patients] vs 24.8% [59 of 238]; P = .72). After adjusting for age, GOC completion was found to be associated with the presence of mechanical ventilation (odds ratio [OR], 6.42; 95% CI, 3.49-11.81) and meeting multiple serious illness criteria (OR, 4.07; 95% CI, 2.25-7.38).The findings of this cohort study suggest that, despite the presence of national guidelines, GOC discussions for patients with serious illness were documented infrequently. This study suggests a need for system-level interventions to ensure best practices and may inform strategies to measure and improve trauma service quality in palliative care.
Long covid update for primary care should acknowledge functional symptoms
Authors: Peter W Ward
Journal: BMJ (2022)

It must be a fraught task, writing about long covid.The list of symptoms is huge and we don't really know how it arises.I often feel inadequate faced with patients distressed by their long covid symptoms.I was bothered by the lack of any mention by Greenhalgh and colleagues of a functional element to long covid. 1 It seemed a huge omission to me.Many of the complaints we see in primary care are of a functional nature and there is often a large functional component to physical illnesses like chronic obstructive pulmonary disease, asthma, heart disease, and musculoskeletal pains.How can we start to help people who suffer functional symptoms if there is a taboo about mentioning it?People with functional symptoms are suffering in the same way as those with physical symptoms and if we are to destigmatise this area of medicine then authors as important and respected as Greenhalgh and colleagues should acknowledge their existence.It would be extraordinary if many people suffering long covid did not have a functional element to their presentations.Concentrating on physical tests and bodily mechanisms wholly risks missing this component.